Why would RC take 3 days at sea on a 7 day cruise and then only spend from 3-10 at a port? I thought I found a good cruise for Thanksgiving and then saw we weren't getting into Puerto Rico till dinner and then leaving before bed! That seems like a waste of a port as I'm sure many things to see are closing down and I don't particularly like going to new places at night.

There are a lot of factors that go into determining a ship's itinerary. It's not the ship's captain saying, "I think we'll go to Puerto Rico just for a few hours at night that day." Every port has a set number of piers at which the ships can dock. It could be that there is no available docking space the day before or that day, until 3pm. Some governments, like Bermuda, limit the number of cruise ships that can be in port at the same time.

It's probably more a case of Royal Caribbean being told, "The only time we can accommodate this particular ship is 3-10pm. Take it or leave it." It's likely that other Royal Caribbean ships will be docked in Puerto Rico that day; perhaps there is a limit to how many ships from the same cruise line can use up dock space at the same time.

Another consideration are tides. The ships have a window of opportunity for arriving into port and leaving, according to the tides and sea conditions.

I'm sure there are other considerations as well that I'm not aware of or not thinking of. It's not usually a case of some suit at Royal Caribbean saying let's allow the passengers of this ship to be in port just a few hours.

The distance between Miami and San Juan is around 900 nautical miles. It takes about 45 hours for a cruise ship to travel that distance. If the Freedom Of The Seas left Miami at 4:30pm and headed for San Juan that would put the ship in port in the early afternoon two days later.

Those reasons sound like a company line to me. On my Honeymoon cruise (1994 on another cruise line) we got to San Juan at a regular time like any other port. As I have watched cruises expand over the years the San Juan stop has become a joke. I believe the cruise industry needs to take more of a stand against this. This is not some foreign country. Royal Caribbean and other lines should be able to negotiate a better time. Take the stop away for a while and see if they change their tune.

I'll phrase this with a definite "I think".
Remember, RCCL is NOT an American Company, and the ships are registered "Bermuda"?
And I agree with Dave that the ports MAY not be able to handle ships the size if Freedom and Liberty, and the other Voyager class ships due to port depth, ship's draft, and tides. I thought that I have even seen that RCCL ships that leave for the Southern routes even leave San Juan late at night-there has to be a reason.
Then again, that's why I'm good at my job and NOT a cruise line owner. Although I tend to be cynical, I also try to NOT see the "Black Helicopters" in everything that doesn't fly the way I think. If I don't like something, I don't do it again; simple as that.
Hope you have a great time anyhow!

Ok, I can understand the port thing as far as waiting your turn- esp since PR is an origin port as well. However will there be things to do, safe things to do that late in the day? We were hoping to do some historic type tours but I remember Nassau shuttered up at 5, except for Senor Frogs and we aren't the party types.
I think I would be hesitiant to head out on an excursion at 4-5 in the afternoon.

On my Honeymoon cruise (1994 on another cruise line) we got to San Juan at a regular time like any other port.

If you cruised from Florida and San Juan was your first stop, then you had two at-sea days enroute, and not a day and a half. It isn't a company line - it is the simple fact that 900 nautical miles takes time to traverse. Ships are faster now than they were in 1994 too. Most modern ships can cruise at 20 to 23 knots. In 1994 the common speed was 18 to 19 knots.